Results 41 to 50 of about 1,296,938 (317)

Optimal alignments of longest common subsequences and their path properties [PDF]

Bernoulli 2014, Vol. 20, No. 3, 1292-1343, 2014
We investigate the behavior of optimal alignment paths for homologous (related) and independent random sequences. An alignment between two finite sequences is optimal if it corresponds to the longest common subsequence (LCS). We prove the existence of lowest and highest optimal alignments and study their differences.
arxiv   +1 more source

A two-base encoded DNA sequence alignment problem in computational biology [PDF]

, 2009
The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics.
Chang, Jen-Mei, Drakes, Chiaka, Huang, Erya, Langat, Deidrey, McGrath, Joseph, Morabito, Mark, Pacheco, Jose, Rodriguez, Nancy, Salazar, Daniel, Vemuri, Rao, Vu, Man, Wadhar, Hem, Wu, Qin   +12 more
core  

Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing [PDF]

, 2003
Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological
Gilbert, D, Westhead, DR, Williams, A
core   +1 more source

Detailed kinship estimation for detecting bias among breeding families in a reintroduced population of the endangered bagrid catfish Tachysurus ichikawai

Population Ecology, EarlyView.
In the process of captive breeding and reintroduction of endangered animal species, it is crucial to minimize familial bias in reproductive success during the reintroduction phase to preserve genetic diversity. In this study, we attempted to identify the familial lineage of individuals of the endangered bagrid fish Tachysurus ichikawai born at the ...
Hinano Mizuno, Kouji Nakayama, Tetsuya Akita, Yasuyuki Hashiguchi, Tomonori Osugi, Hirohiko Takeshima   +5 more
wiley   +1 more source

Optimal SNP filtering strategies for pedigree reconstruction: A case study with wild red‐spotted masu salmon population

Population Ecology, EarlyView.
In this article, we tested optimal SNP filtering strategies for accurate parentage assignment and pedigree reconstruction for a wild population of red‐spotted masu salmon, Oncorhynchus masou ishikawae. We found that mid‐point filtering in terms of call rate and minor allele frequency performs well for pedigree reconstruction.
Shohei Noda, Tetsuya Akita, Rui Ueda, Takafumi Katsumura, Yasuyuki Hashiguchi, Hirohiko Takeshima, Takuya Sato   +6 more
wiley   +1 more source

Linking GPS and travel diary data using sequence alignment in a study of children's independent mobility

International Journal of Health Geographics, 2011
Background Global positioning systems (GPS) are increasingly being used in health research to determine the location of study participants. Combining GPS data with data collected via travel/activity diaries allows researchers to assess where people ...
Mavoa Suzanne, Oliver Melody, Witten Karen, Badland Hannah M   +3 more
doaj   +1 more source

Pairwise alignment incorporating dipeptide covariation

, 2005
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated.
Altschul, Altschul, Altschul, Altschul, Bailey, Bishop, Brenner, Cline, Crooks, DOOLITTLE, Frith, Fukami-Kobayashi, G. E. Crooks, Goldman, Gonnet, Henikoff, Henikoff, Jung, Karplus, Lin, Muller, Murzin, Park, Pearson, R. E. Green, RODIONOV, S. E. Brenner, Sander, Smith, Thorne, Thorne, Thorne, Topham, Weiss, Zachariah   +34 more
core   +1 more source

Evaluating the origin and spread of spotted lanternfly (Lycorma delicatula) in Japan

Population Ecology, EarlyView.
The invasive spotted lanternfly (Lycorma delicatula) is native to China and is a serious economic pest in the Republic of Korea and the United States, though it is not considered a pest in Japan. We established a distribution map of L. delicatula in Japan through a comprehensive review of published literature and citizen science reports and analyzed ...
Matthew T. Kamiyama, Michihiko Takahashi, Hannah J. Broadley, Francesc Gómez‐Marco, Mark S. Hoddle, Kenji Matsuura   +5 more
wiley   +1 more source

Lower bounds on multiple sequence alignment using exact 3-way alignment

BMC Bioinformatics, 2007
Background Multiple sequence alignment is fundamental. Exponential growth in computation time appears to be inevitable when an optimal alignment is required for many sequences. Exact costs of optimum alignments are therefore rarely computed. Consequently
Colbourn Charles J, Kumar Sudhir
doaj   +1 more source

Metric Learning for Temporal Sequence Alignment [PDF]

, 2014
In this paper, we propose to learn a Mahalanobis distance to perform alignment of multivariate time series. The learning examples for this task are time series for which the true alignment is known.
Arlot, Sylvain, Bach, Francis, Garreau, Damien, Lajugie, Rémi   +3 more
core   +3 more sources